Hello Kyle,
The duplicate buses have been removed from TransitView as of yesterday. After reviewing your comment, we found this only occurred when the trip_id for that bus did not have a corresponding trip in the GTFS. Unfortunately, there are a handful of such buses. With school in session, a number of them are probably school trips so you might have noticed more duplicates in the morning and early afternoon.
The old code behind TransitView would show non-revenue (deadhead) buses as orange. Those buses have been filtered out for a little while now. There is one exception to that, however, route 35. Since this route is listed internally as a loop, it doesn't have an East, West, North, or South designation and defaults to orange.
As for the 12AM disappearing buses, have you noticed this happening on a specific route or time? Is it during the transition from 11:59 to 12:00AM on the weekday or have you noticed this on the weekend? This also might have been related to the duplicate bus issue that was fixed yesterday. We will continue to review our midnight logs for the rest of the week to see if we can catch this happening.
-Greg